When GSX is installed the FSX.cfg file is modified to have simobjects point to the proper GSX directory
When GSX is installed, the FSX.CFG file is modified to ADD its own Simobject paths to the *existing* paths so, it will surely not remove the standard airplanes, but will add them to it.
When GSX is uninstalled, FSX.cfg is NOT modified back. I corrected the entries back to the original and now SE:FSX runs as before.
That's not an error, of course. Since the Simobject in the Addon Manager folder are shared by all FSDT products, just uninstalling GSX won't remove their path, otherwise the sceneries won't work anymore. However, this couldn't possibly result in your default objects ( Airplanes, etc. ), because as I've said, the paths to the GSX objects were ADDED to the existing paths, not replaced.
The only possible explanation for the paths to your original objects being removed, is that your FSX.CFG was already corrupted, or contained any kind of syntax error, usually resulting from having edited by hand, but also by being corrupted by 3rd party utilities that access to it.
GSX surely cannot be the cause, since nobody ever reported losing his airplanes "just" by installing GSX.